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- PDB-6o88: Crystal Structure of UDP-dependent glucosyltransferases (UGT) fro... -

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Basic information

Entry
Database: PDB / ID: 6o88
TitleCrystal Structure of UDP-dependent glucosyltransferases (UGT) from Stevia rebaudiana in complex with UDP and rebaudioside A
ComponentsUDP-glycosyltransferase 76G1
KeywordsTRANSFERASE / plant biochemistry
Function / homology
Function and homology information


UDP-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases
Similarity search - Function
UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-LRV / URIDINE-5'-DIPHOSPHATE / UDP-glycosyltransferase 76G1
Similarity search - Component
Biological speciesStevia rebaudiana (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å
AuthorsLee, S.G. / Jez, J.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Molecular basis for branched steviol glucoside biosynthesis.
Authors: Lee, S.G. / Salomon, E. / Yu, O. / Jez, J.M.
History
DepositionMar 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-glycosyltransferase 76G1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2983
Polymers52,0871
Non-polymers1,2112
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: UDP-glycosyltransferase 76G1
hetero molecules

A: UDP-glycosyltransferase 76G1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,5966
Polymers104,1742
Non-polymers2,4224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area3480 Å2
ΔGint-30 kcal/mol
Surface area33780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.118, 98.118, 91.524
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein UDP-glycosyltransferase 76G1


Mass: 52087.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stevia rebaudiana (plant) / Gene: UGT76G1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6VAB4, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-LRV / (8alpha,9beta,10alpha,13alpha)-13-{[alpha-L-allopyranosyl-(1->2)-[beta-D-mannopyranosyl-(1->3)]-beta-D-allopyranosyl]oxy}kauran-18-oic acid


Mass: 806.888 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H62O18
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% (w/v) PEG-4000, 20% 2-propanol (v/v), 100 mM sodium citrate tribasic dihydrate buffer pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.99→42.5 Å / Num. obs: 35139 / % possible obs: 99.5 % / Redundancy: 4.7 % / Net I/σ(I): 25.9
Reflection shellResolution: 1.99→2.02 Å / Num. unique obs: 35139 / Rpim(I) all: 0.04 / Rsym value: 0.093

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
PHASERphasing
Cootmodel building
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.99→42.49 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.29
RfactorNum. reflection% reflection
Rfree0.2 1751 4.99 %
Rwork0.164 --
obs0.165 35107 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.99→42.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3548 0 81 212 3841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073737
X-RAY DIFFRACTIONf_angle_d1.035091
X-RAY DIFFRACTIONf_dihedral_angle_d13.6382209
X-RAY DIFFRACTIONf_chiral_restr0.159567
X-RAY DIFFRACTIONf_plane_restr0.005641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9904-2.04420.2611340.2142401X-RAY DIFFRACTION94
2.0442-2.10440.27751160.21122509X-RAY DIFFRACTION99
2.1044-2.17230.24091370.18662558X-RAY DIFFRACTION100
2.1723-2.24990.22791220.17662568X-RAY DIFFRACTION100
2.2499-2.340.22721380.17862545X-RAY DIFFRACTION100
2.34-2.44650.23291590.16872547X-RAY DIFFRACTION100
2.4465-2.57540.2251420.16392556X-RAY DIFFRACTION100
2.5754-2.73680.22341330.16322559X-RAY DIFFRACTION100
2.7368-2.9480.20821260.17582577X-RAY DIFFRACTION100
2.948-3.24460.20561180.16952600X-RAY DIFFRACTION100
3.2446-3.71390.21661300.15762614X-RAY DIFFRACTION100
3.7139-4.67820.16051460.13652611X-RAY DIFFRACTION100
4.6782-42.4960.17031500.16122711X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.98350.1514-0.54241.159-0.33380.45150.05130.09310.1602-0.02750.0059-0.0286-0.15370.04880.00010.2325-0.04370.05490.19780.00490.180235.8542-7.49294.6561
21.33590.24870.34180.4770.0260.5358-0.00820.15150.0369-0.17090.0709-0.0767-0.02840.065800.2517-0.00570.07580.17780.01940.205126.2183-23.7951-5.9068
32.13450.1369-0.16970.749-0.31770.5561-0.0030.16730.045-0.17340.0401-0.00340.0458-0.115500.2048-0.0030.01470.17130.01380.145812.8904-24.5227-1.7991
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 12 THROUGH 148 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 149 THROUGH 288 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 289 THROUGH 458 )

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